Contacts of the strand formed by residues 580 - 584 (chain A) in PDB entry 3I5H
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PHE 580 (chain A).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A LEU* 4.8 0.7 - - + -
532A ILE* 3.3 36.6 - - + -
554A LEU* 4.5 9.2 - - + -
555A TYR* 4.5 0.4 - - + -
565A PHE* 3.0 42.4 - + + -
566A GLY 3.4 8.7 - - - +
568A PRO* 3.6 11.4 - - - +
579A HIS* 1.3 87.4 - - + +
581A CYS* 1.3 58.4 + - - +
582A LEU* 3.7 13.9 - - + -
590A SER* 4.4 0.2 - - - -
591A TYR* 2.7 63.9 + + + +
593A ILE* 3.8 24.2 - - + -
596A TRP* 4.2 10.5 - + - -
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Residues in contact with CYS 581 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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564A MET 3.3 2.5 - - - +
565A PHE* 3.6 2.4 - - - -
566A GLY* 2.9 47.6 + - - -
567A LYS* 3.9 8.5 - - - -
568A PRO* 4.7 3.6 - - + -
580A PHE* 1.3 75.8 - - - +
582A LEU* 1.3 64.7 + - - +
588A SER* 4.0 15.3 - - - +
589A VAL 3.0 20.4 - - - +
590A SER* 3.8 15.9 - - - +
591A TYR* 4.6 0.7 - - - -
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Residues in contact with LEU 582 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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478A LEU* 3.5 26.5 - - + -
522A CYS* 4.5 6.5 - - - -
525A LEU* 3.2 34.5 - - + -
526A ILE* 4.6 9.2 - - + -
532A ILE* 3.4 30.3 - - + -
564A MET 3.3 5.4 - - - +
565A PHE* 4.0 5.6 - - + -
580A PHE* 3.7 10.8 - - + -
581A CYS* 1.3 81.6 - - - +
583A HIS* 1.3 59.4 + - - +
584A HIS* 3.7 21.7 + - + +
588A SER* 3.5 7.4 + - - -
589A VAL 3.0 28.6 + - - -
591A TYR* 3.9 4.5 - - + -
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Residues in contact with HIS 583 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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485A GLU* 4.6 0.3 - - - +
518A ASP 5.7 5.4 + - - -
519A LEU* 6.2 3.1 - - + -
522A CYS* 3.8 19.2 - - - +
563A PRO 5.4 1.6 - - - +
564A MET* 3.4 44.3 + - + +
582A LEU* 1.3 73.6 - - - +
584A HIS* 1.3 66.3 + - - +
585A TYR* 4.1 3.9 + - - -
587A GLY* 3.7 13.4 - - - -
588A SER* 4.7 5.6 - - - +
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Residues in contact with HIS 584 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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467A PHE* 3.4 34.5 - + + -
478A LEU* 4.8 0.4 - - + -
481A ASN* 3.6 18.4 - - + +
485A GLU* 2.6 27.2 + - + +
522A CYS* 3.4 18.0 - - - -
526A ILE* 4.7 7.2 - - + -
582A LEU* 3.9 18.5 - - + +
583A HIS* 1.3 79.1 + - - +
585A TYR* 1.3 53.3 + - - +
586A ALA 2.5 2.2 + - - +
587A GLY* 2.4 44.1 + - - +
589A VAL* 3.7 17.7 - - + -
591A TYR* 2.7 34.2 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il